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All functions

allocateCells()
Annotate all cells with contour level of cell type-specific density.
cellsInRegion()
Check which cells are in which regions
computeDensity()
Perform kernel density estimation on SpatialExperiment
computeDensityHex()
Perform kernel density estimation on SpatialExperiment
contour2sf()
Draw a contour region on some density level
corDensity()
Test for density correlation between two cell types.
findROI()
Find ROIs based on cell type-specific densities via graph-based method.
getContour()
Get contour from density
getContourRegions()
Calculate areas between every two density levels
grid2sf()
Convert x,y nodes to sf polygons
gridDensity()
Perform kernel density estimation on SpatialExperiment for cell types of interest
gridSPE()
Summarize a SpatialExperiment object at grid-level
mergeROI()
Manually merge ROIs
plotCellCompo()
Plot cell type composition in each density level of cell of interest.
plotContour()
Plot contour lines.
plotContourRegion()
Visualising an sf object (for internal use only at the moment)
plotCorHeatmap()
Plot model statistics using heatmap.
plotDensCor()
Plot density correlation between two cell types
plotDensity()
Plot grid-based density.
plotGrid()
Plot grid from metadata.
plotROI()
Plot ROIs on spatial.
plotSpatial()
Plot cells based on spatial coordinates.
postSelRegion()
Merge sel_region from the selectRegion function to SpatialExperiment.
selectRegion()
Select region of interest from plot
spe2PB()
Given a 'SpatialExperiment' data object, create pseudo-bulk samples using the colData information and return a DGEList object
`[`(<SpatialExperiment>,<ANY>,<ANY>,<ANY>)
Subset for grid level analysis